Fate, clonal evolution, and therapeutic vulnerabilities of BRCA1-deficient cells in early breast tumorigenesis

Germline BRCA1 mutations represent the most common cause of hereditary breast cancer. BRCA1 is essential for homologous recombination–mediated DNA repair, and loss of heterozygosity (LOH) abrogates its function, driving tumor initiation and progression. Because early detection strategies and effective prevention alternatives to prophylactic mastectomy remain lacking, understanding the genomic and regulatory programs governing survival and clonal expansion of BRCA1-deficient cells is critical. To address this, we developed a detectable conditional knockout model of BRCA1 (BRCA1-DCO) in which LOH is genetically coupled to irreversible mTmG reporter switching, enabling fate tracking of BRCA1-knockout cells at single-cell resolution. Whole mount mammary gland imaging revealed that concurrent Trp53 loss is required for survival of BRCA1-deficient epithelial cells, and that the microenvironment responds to BRCA1 loss through rapid innate immune infiltration. However, we show that PARP inhibition combined with immune checkpoint blockade suppresses, but does not fully eradicate, BRCA1-deficient cells, highlighting the need for improved targeted interventions. Using this model, we integrate genomic evolution and clonal dynamics (scWGS) and epigenetic and transcriptional states to investigate survival and early progression of BRCA1-LOH epithelial cells, with the goal of identifying candidate therapeutic targets for chemopreventive intervention.